Assessing the use of mitochondrial cox1 gene and cox2-3 spacer for genetic diversity study of Malaysian Gracilaria changii (Gracilariaceae, Rhodophyta) from Peninsular Malaysia

Yow, Yoon‐Yen; Lim, Phaik-Eem; Phang, Siew‐Moi

doi:10.1007/s10811-012-9942-x

Cited by 26 publications

(15 citation statements)

References 66 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Agardh (1847: 16) and Kappaphycus Doty (1988: 171) (Conklin et al 2009), Portieria Zanardini (1851: 33) (Payo et al 2012), Fredericqia Maggs, Le Gall, Mineur, Provan & G.W. Saunders (2013: 284) (Maggs et al 2013), Gracilaria Greville (1830: LIV, 121) (Yow et al 2013) and Bangia Lyngbye (1819: 82) (Shea et al 2014). Conversely, for Ahnfeltiopsis pusilla (Montagne 1834: 287) P.C.…”

Section: Introductionmentioning

confidence: 99%

Analysis of the cox2-3 spacer region for population diversity and taxonomic implications in rhodolith-forming species (Rhodophyta: Corallinales)

et al. 2014

View full text Add to dashboard Cite

Coralline red algae demonstrate phenotypic plasticity related to environmental factors, rendering their identification difficult. The cox2-3 spacer is a mitochondrial marker widely used for phylogeographic studies and discrimination between closely related species in red algae; however, cox2-3 spacer sequence data for coralline algae are still limited. In this study we substantially increase the number of cox2-3 spacer sequences available for coralline algae, exploring their usefulness for different types of molecular investigations in coralline algae (DNA barcoding and phylogeography), with emphasis on rhodolith-forming species. Specimens from North Atlantic Europe, the Caribbean region and the Gulf of California (Mexico) were sequenced and two datasets were built, one for the subfamily Lithophylloideae and one for the Melobesioideae. Our results suggest the utility of cox2-3 spacer as barcoding marker for coralline algae with a slight variation in the barcode gap depending in the way gaps in the alignment are treated. Analyses on both datasets found a barcode gap or separation between intra and interspecific divergence (p distance and ABGD analysis) while some inconsistencies were evident when the results were compared with morphology-based classification. Using the cox2-3 spacer region, the morphospecies Lithophyllum margaritae from the Gulf of California revealed the existence of two well-supported clades, with the possibility of respectively five and two additional species; haplotype networks for Phymatolithon calcareum and P. purpureum revealed similar patterns when Mediterranean and NW Europe specimens were analysed, and P. calcareum was shown to consist of a single population in NW Europe. Based on our analyses the marker cox2-3 spacer has strong potential applications for studies of phylogeography and DNA barcoding in coralline algae after understanding its variation.

show abstract

Section: Introductionmentioning

confidence: 99%

Analysis of the cox2-3 spacer region for population diversity and taxonomic implications in rhodolith-forming species (Rhodophyta: Corallinales)

et al. 2014

View full text Add to dashboard Cite

show abstract

“…Different molecular markers have been employed in studies of phylogeny and genetic diversity of Gracilariales; these include mitochondrial markers, like COI (Yang et al 2008;Yow et al 2011Yow et al , 2013 and the cox2-cox3 spacer (Rueness 2005;Destombe et al 2010;Pareek et al 2010;Garcı´a-Rodrı´guez et al 2013;Yang et al 2013); plastidencoded markers, like the RuBisCo spacer (Destombe & Douglas 1991;Byrne et al 2002;Iyer et al 2005;Guillemin et al 2008) and rbcL M.S. Kim et al 2006); and nuclear markers, like ITS (Goff et al 1994).…”

Section: Introductionmentioning

confidence: 99%

Genetically recognizable but not morphologically: the cryptic nature ofHydropuntia corneaandH. usneoides(Gracilariales, Rhodophyta) in the Yucatan Peninsula

et al. 2015

View full text Add to dashboard Cite

Species recognition in algae is often extremely difficult due to the paucity of morphological characters and high environmental plasticity. If environment is important to morphology, then related species growing in sympatry are good candidates to discover diagnostic characters. We studied algae collected in sympatric populations in tropical Atlantic Mexico. Hydropuntia cornea and H. usneoides have high morphological variation and have been difficult to diagnose morphologically. We used four molecular markers (RuBisCo spacer, cox2-3 spacer, rbcL and COI) to investigate the genetic relationship between samples that correspond to either H. cornea or H. usneoides; in addition, we determined if molecular-characterized groups were morphologically distinguishable. RuBisCo and cox2-3 spacers revealed low genetic variation but showed two genetic groups: groups I and II. rbcL and COI phylogenies also showed a separation into two groups, corresponding with cox2-3 spacer groups I and II. Group I matched sequences in GenBank of H. usneoides and group II with H. cornea. Populations were mixed for these genetic groups, with group I prominent in Quintana Roo populations. Morphological analysis of samples in both genetic clades showed that they are not distinguishable. As the difference between the two groups is only genetic, they are, consequently, cryptic species. While the extremes of morphology in allopatric populations may be distinguishable, we do not feel that in most cases these species can be recognized. Therefore, we propose that these two 'species' should be designated as a species complex (the Hydropuntia cornea/H. usneoides complex).

show abstract

“…Such oceanographic conditions could have promoted genetic connectivity in marine taxa. To date, reports on the genetic structure and phylogeography inferred from marine algal species in Malaysia (Yow et al 2011(Yow et al , 2013.…”

Section: Introductionmentioning

confidence: 99%

Small-scale genetic structure of Gracilaria salicornia and its red algal parasite, G. babae (Gracilariaceae, Rhodophyta), in Malaysia

Lim

Phang

2015

Botanica Marina

Self Cite

View full text Add to dashboard Cite

The present study compares genetic structure from the plastid rbcL, mitochondrial cox1, and nuclear internal transcribed spacer (ITS) sequences among 13 populations of Gracilaria salicornia and its red algal parasite, G. babae, in Malaysia. Owing to the unique biology of the red algal parasite, identical phylogeographies were inferred from the rbcL and cox1 sequences in both G. babae and its host, G. salicornia. Despite the low genetic variation, rbcL and cox1 showed a concordant phylogeographic split that largely corresponds to Peninsular Malaysia and East Malaysia, except for a sample from East Malaysia that was consistently grouped with samples from the peninsula. On the other hand, G. salicornia was separated from G. babae in the midpoint-rooted phylogeny inferred from ITS data despite the failure to retrieve the two taxa in reciprocal monophyly. Gracilaria salicornia was less diverse and lacked apparent geographic structure. In contrast, the ITS data revealed considerable genetic diversity and fine-scale genetic structuring in G. babae within Malaysian waters, probably as a result of adaptation to the local host population.

show abstract

Assessing the use of mitochondrial cox1 gene and cox2-3 spacer for genetic diversity study of Malaysian Gracilaria changii (Gracilariaceae, Rhodophyta) from Peninsular Malaysia

Cited by 26 publications

References 66 publications

Analysis of the cox2-3 spacer region for population diversity and taxonomic implications in rhodolith-forming species (Rhodophyta: Corallinales)

Analysis of the cox2-3 spacer region for population diversity and taxonomic implications in rhodolith-forming species (Rhodophyta: Corallinales)

Genetically recognizable but not morphologically: the cryptic nature ofHydropuntia corneaandH. usneoides(Gracilariales, Rhodophyta) in the Yucatan Peninsula

Small-scale genetic structure of Gracilaria salicornia and its red algal parasite, G. babae (Gracilariaceae, Rhodophyta), in Malaysia

Contact Info

Product

Resources

About